9LPE | pdb_00009lpe

ATPDF2 HDZIP domain complexed with DNA

• PDB DOI: https://doi.org/10.2210/pdb9LPE/pdb
• NAKB: 9LPE

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-01-24 Released: 2025-12-03 
• Deposition Author(s): Chen, W., Huang, H.D.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 
  0.282 (Depositor), 0.315 (DCC) 
• R-Value Work: 
  0.274 (Depositor), 0.286 (DCC) 
• R-Value Observed: 
  0.276 (Depositor) 

Starting Model: in silico

Literature

Molecular insights into DNA recognition by HD-Zip transcription factors.

Chen, W., Yan, W., Jiang, K., Huang, H.

(2025) Plant Physiol 198

• PubMed: 40583771 
• DOI: https://doi.org/10.1093/plphys/kiaf292
• Primary Citation of Related Structures:  
  9LPE


• PubMed Abstract: 
  

  Homeodomain-leucine zipper (HD-Zip) genes encode a large family of plant-specific transcription factors (TFs) that are integral to plant development, growth, regulation, and responses to environmental and hormonal signals. While the roles and mechanisms of HD-Zip TFs have been extensively studied, the structural basis for their DNA recognition remains unclear. In this study, we analyzed DAP-seq data and identified consensus DNA motifs, 5'-AAT[W]AT-3' and 5'-[N]AAA[N][N]-3', preferentially bound by HD-Zip TFs. Both motifs feature a 5'-AA(T/A)-3' core, which is shared across previously identified HD-Zip target sequences, suggesting a common recognition feature within the HD-Zip family. Focusing on the well-characterized HD-Zip IV TF PROTEIN PRODUCTION FACTOR 2 (PDF2) from Arabidopsis (Arabidopsis thaliana) and its interaction with the L1 box DNA sequence, our structural and biochemical analyses revealed that the PDF2 HD-ZA module forms a dimer to specifically recognize the 5'-AATG-3' core through an asymmetric binding mode. In this mode, only the primary recognition helix of 1 protomer and the N-arm of the other protomer in the PDF2 HD-ZA dimer are involved in specific DNA interactions. Our study offers insights into the molecular mechanisms of HD-Zip TFs and provides a structural template for engineering applications in agricultural research.

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Organizational Affiliation: 
• Institute for Biological Electron Microscopy, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
New Cornerstone Science Laboratory, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
Laboratory of Cell Metabolism and Diseases, State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650500, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.95 kDa 
• Atom Count: 2,058 
• Modeled Residue Count: 186 
• Deposited Residue Count: 260 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox-leucine zipper protein PROTODERMAL FACTOR 2	A, B	112	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PDF2
UniProt
Find proteins for Q93V99 (Arabidopsis thaliana) Explore Q93V99  Go to UniProtKB:  Q93V99

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*AP*AP*AP*TP*GP*CP*AP*GP*TP*GP*CP*AP*TP*TP*TP*A)-3')	C	18	Arabidopsis thaliana

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*AP*AP*AP*TP*GP*CP*AP*CP*TP*GP*CP*AP*TP*TP*TP*A)-3')	D	18	Arabidopsis thaliana

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free:  0.282 (Depositor), 0.315 (DCC) 
• R-Value Work:  0.274 (Depositor), 0.286 (DCC) 
• R-Value Observed: 0.276 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.278	α = 90
b = 73.278	β = 90
c = 170.788	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Chen, W., Huang, H.D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	NSFC Grant No. 31930096 and 1902034

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release